Excessive deflection of a rail in response to axle loading can lead to discomfort for passengers and increased wear of both railway structures and trains. These oscillations are often caused by poor trackbed stiffness which may be due to either soft subgrade and/or contaminated ballast. A variety of trackbed stabilisation (TBS) techniques are available to remediate soft subgrades and increase the safety of tracks within the railway network. Traditional TBS methods require track removal, which is expensive, disruptive and often inefficient maintenance works. Micro-piling, using screw piles installed between sleepers, is an innovative low disruption TBS technique. This paper investigates the performance of a soft subgrade and contaminated ballast section of rail line in the UK, before and after screw pile TBS. Pre and post remediation, a computer vision-based system was used to measure rail vertical deflections during train passages and then analysed to quantify the trackbed stiffness. Additionally, 3D finite element models are created and validated by the site measurements. The finite element models are used to simulate a range of different scenarios exploring how changes to the TBS piling layout and/or further works, such as ballast improvement could add further improvements or design efficiencies. Site measurements show TBS reduced rail deflection by 20–30%, indicating that micro-piling is an effective technique for soft subgrades. The finite element analysis revealed the efficiency of micro-piling is highly dependent on the conditions of ballast, strength of the ground at the pile toe, and the pile arrangement. When the aforementioned are optimised the rail deflection could be reduced to approximately 50% of the pre TBS condition.